The chromosome-scale genome provides insights into pigmentation in Acer rubrum

ArMYB89 and ArCOP1 interaction modulates anthocyanin biosynthesis in Acer rubrum leaves under low-temperature conditions

Acer rubrum, a famous ornamental tree, produces bright red-coloured leaves because of the temperature decline from summer to autumn. This process's molecular mechanism is elusive, so we have investigated how anthocyanin biosynthesis is induced in A. rubrum leaves under low temperatures. The results of low-temperature treatment under light and dark conditions showed that the low-temperature promoted anthocyanin accumulation in A. rubrum is light-dependent. The transcriptome analysis showed that ArMYB89 was significantly highly expressed in leaves of A. rubrum growing under low temperatures with light conditions. The findings from the Dap-seq analysis, yeast one hybridisation, electrophoretic mobility shift assay and luciferase reporter assay indicated that the ArMYB89 transcription factor binds directly to the promoter of ArUGT52 and stimulates its transcription. The co-expression of ArUGT52 with ArMYB89 significantly induced anthocyanin levels under low temperatures with light conditions. Enzyme activity analysis showed that ArUGT52 could convert Cyanidins and Pelargonidins into Cyanidin-3-O-glucoside and Pelargonidin 3-glucoside, which are considered the main anthocyanins in red colour leaves of A. rubrum. The results of yeast two hybridisation, pulldown assay and bimolecular fluorescence complementation experiment showed an interaction between COP1 and ArMYB89, while in vivo and in vitro protein ubiquitination assay demonstrated that ArCOP1 ubiquitinates ArMYB89. Notably, co-expression of ArCOP1 with ArMYB89 significantly reduced anthocyanin levels, while the virus-induced gene silencing of ArCOP1 significantly induced anthocyanin levels under low temperatures with light conditions. In conclusion, this work revealed the molecular mechanism regulating anthocyanin accumulation in the A. rubrum leaves under low temperatures.

ArNAC148 induces Acer rubrum leaf senescence by activating the transcription of the ABA receptor gene ArPYR13

Acer rubrum, an ornamental tree known for its stunning autumn colors, has an elusive molecular mechanism that governs its leaf senescence. We performed the genome-wide analysis of NAC transcription factor genes and PYRABACTIN RESISTANCE1-LIKE (PYLs) and found that ArNAC148 and ArPYL13 were significantly upregulated in senescing leaves as compared to mature leaves. Subcellular localization studies confirmed the nuclear localization of ArNAC148 and the cytoplasmic localization of ArPYL13. Electrophoretic mobility shift assay and yeast one-hybrid assay demonstrated that ArNAC148 directly binds to the promoter of ArPYL13. Luciferase reporter assays further showed that ArNAC148 activates the transcription of ArPYL13. The transient expression of ArNAC148 and ArPYL13 in tobacco leaves promoted chlorophyll degradation, increased H2O2 level, MDA contents, and electrolyte leakage in response to abscisic acid (ABA). Moreover, the virus-induced gene silencing of ArNAC148 and ArPYL13 in A. rubrum produced results that were opposite to those observed in transient expression experiments. Our findings suggest that ArNAC148 induces leaf senescence by directly activating the transcription of ArPYL13, providing insights into the ABA-mediated regulatory mechanisms governing leaf senescence in A. rubrum. This study offers new perspectives for researchers to explore the roles of NAC and PYL genes in regulating leaf senescence in woody ornamental plants.

Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology

DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.